What is Epigenetics technical articles are geared towards epigenetic research techniques, news, and trends in the field of epigenetics, written by scientists from universities and institutions including UCLA, Hofstra, NIH, Johns Hopkins, and more.

Explore in detail new epigenetic research techniques and tips for topics like next-generation sequencing (NGS) in epigenetics, m6A RNA methylation, CRISPR/Cas9 system epigenetic editing, chromatin immunoprecipitation (ChIP) protocol optimization, and single-cell epigenomics methods.

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Transposase-Accessible Chromatin Assay for Fast and Sensitive Epigenomic Profiling

November 18, 2013 WhatIsEpigenetics

Scientists at Stanford University School of Medicine have developed a rapid and sensitive method for integrative epigenomic analysis called assay for transposase-accessible chromatin using sequencing (ATAC-seq).This assay is based on direct in vitro transposition of sequencing adaptors into native chromatin, which captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. By using ATAC-seq, the scientists discovered classes of DNA-binding [more…]

New Technique Available to Measure m6A Levels for RNA Methylation Studies

October 22, 2013 WhatIsEpigenetics

Researchers at Epigentek recently developed a new and breakthrough approach to identify the “fifth base” of RNA, N6-methyladenosine (m6A) to efficiently study RNA methylation in a practical and cost-effective manner. The technology is based on a high throughput and strip-well microplate format and is made commercially available as the EpiQuik m6A RNA Methylation Quantification Kit, the first of its kind. It was commonly believed that messenger RNA (mRNA) contains four nucleobases — guanine, adenine, uracil, and cytosine. However in 2012, [more…]

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

October 16, 2013 WhatIsEpigenetics

The scientists at MIT describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator–like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, they demonstrated that modification of critical methylated promoter CpG positions can lead to substantial increases in the expression of endogenous human genes. Genome-wide studies have defined cell type–specific patterns of DNA methylation that are important for regulating gene expression in both normal development2 [more…]

DNMT1-Interacting RNAs Block Gene-Specific DNA Methylation

October 16, 2013 Milka Rodriguez

5-methylcytosine is found in the context of paired symmetrical methylation of a CpG site. In normal somatic cells, most CpG sites are heavily methylated, while CpG islands (sites of CpG clusters) in germ-line tissues and located near promoters, remain unmethylated thus allowing gene expression to occur.  When a CpG island in the promoter region of a gene is methylated, expression of the gene is repressed. The addition of methyl groups is controlled at several different levels in cells and is [more…]

A New Study Shows MicroRNA-26a Targets DNA Demethylation Enzymes

October 16, 2013 WhatIsEpigenetics

In their studies, the scientists at Beckman Research Institute of City of Hope demonstrated that Ten eleven translocation (TET) enzymes and thymine DNA glycosylase (TDG) can be direct targets of the microRNA miR-26a. These DNA demethylation enzymes are down-regulated in islets during postnatal differentiation, whereas miR-26a is up-regulated. They also report that changes in 5-hydroxymethylcytosine accompany changes in TET mRNA levels and over expression of miR-26a in mice increases postnatal islet cell number in vivo and endocrine/acinar colonies in vitro. [more…]

“Post-Bisulfite” and Higher Sensitivity DNA Library Preparation Technology for Epigenetics-Targeted Next Generation Sequencing Analysis

October 4, 2013 WhatIsEpigenetics

Scientists at Epigentek developed a series of new products for DNA library preparation used in next generation sequencing analysis of epigenetic mechanisms including genome-wide DNA methylation and DNA-protein interaction. Next-gen sequencing requires an initial preparation of a DNA library, but often necessitates a high amount of starting materials to achieve. This makes tumor biopsy and embryonic tissue samples especially challenging to sequence for epigenetic applications. Current commercial offerings from other companies are also rather expensive as well as laborious. These [more…]

Novel Assay to Probe the DNA Methylation State of Multiple Genomic Loci in Single Cells

October 1, 2013 WhatIsEpigenetics

The scientists from A*STAR’s Institute of Medical Biology (IMB) and Institute of Molecular and Cell Biology (IMCB)  developed a novel methodology to probe single cells for various DNA-methylation errors at multiple loci to reveal failed maintenance of epigenetic mark results in chimeric mice, which display unpredictable phenotypes leading to developmental arrest. This methodology allows the use of  a special technique utilizing a microfluidic device to safely extract one cell for performing the assay called “pronuclear transfer” to ameliorate reprogramming defects in embryos. This study not [more…]

Chromatin Remodelers Fine-Tune H3K36me-Directed Deacetylation of Neighbor Nucleosomes by Rpd3S

September 30, 2013 Milka Rodriguez

To form chromatin, DNA is tightly wrapped around nuclear proteins called histones. The repeating DNA-histone complex, which consists of 146 base pairs of double-stranded DNA wrapped around eight core histone proteins (H2A, H2B, H3 and H4), is called a nucleosome. Histone proteins are involved in structural organization of chromatin in eukaryotic cells. They can undergo various posttranslational modifications (PTMs) such as methylation/demethylation and acetylation/deacetylation, which can alter their interaction with DNA and nuclear proteins resulting in remodeling of chromatin structure [more…]

Epigenetic Memory at Embryonic Enhancers Identified in DNA Maps from Adult Mouse Tissues

September 13, 2013 Milka Rodriguez

In human DNA, 5-methylcytosine is found in approximately 1.5% of genomic DNA. In somatic cells, 5-mC occurs almost exclusively in the context of paired symmetrical methylation of a CpG site. An exception to this is seen in embryonic stem (ES) cells, where a substantial amount of 5-mC is also observed in non-CpG contexts. In the bulk of genomic DNA, most CpG sites are heavily methylated while CpG islands (sites of CpG clusters) in germ-line tissues and located near promoters of [more…]

Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes

September 13, 2013 WhatIsEpigenetics

Scientists from Japan developed methylation-specific fluorescence in situ hybridization (MeFISH) for microscopic visualization of DNA methylation status at specific repeat sequences in individual cells. MeFISH is based on the differential reactivity of 5-methylcytosine and cytosine in target DNA for interstrand complex formation with osmium and bipyridine-containing nucleic acids (ICON). Cell nuclei and chromosomes hybridized with fluorescence-labeled ICON probes for mouse major and minor satellite repeats were treated with osmium for crosslinking. After denaturation, fluorescent signals were retained specifically at satellite [more…]

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